Mercurial > repos > iuc > microsatbed

annotate find_str.py @ 3:a1336aae0d6d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 891fc6321cd94c9a63c880d75989d79521f1a9b6
author iuc
date Sat, 14 Sep 2024 12:16:51 +0000
parents dee16d45a2a9
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dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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1 import argparse
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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2 import subprocess
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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3
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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4 import pytrf # 1.3.0
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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5 from pyfastx import Fastx # 0.5.2
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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6
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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7 """
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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8 Allows all STR or those for a subset of motifs to be written to a bed file
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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9 Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP.
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a1336aae0d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 891fc6321cd94c9a63c880d75989d79521f1a9b6
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10 Note that there are only four possible types of dinucleotide repeat, because CA = AC = GT = TG, GA = AG = CT = TC, AT = TA, and GC = CG.
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dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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11 """
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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12
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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14 def getDensity(name, bed, chrlen, winwidth):
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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15 """
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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16 pybigtools can write bigwigs and they are processed by other ucsc tools - but jb2 will not read them.
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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17 Swapped the conversion to use a bedgraph file processed by bedGraphToBigWig
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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18 """
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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19 nwin = int(chrlen / winwidth)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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20 d = [0.0 for x in range(nwin + 1)]
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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21 for b in bed:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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22 nt = b[5]
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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23 bin = int(b[1] / winwidth)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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24 d[bin] += nt
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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25 bedg = [
3
a1336aae0d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 891fc6321cd94c9a63c880d75989d79521f1a9b6
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26 (name, (x * winwidth), ((x + 1) * winwidth), float(d[x]))
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dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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27 for x in range(nwin + 1)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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28 if (x + 1) * winwidth <= chrlen
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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29 ]
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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30 return bedg
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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31
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32
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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33 def write_ssrs(args):
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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34 """
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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35 The integers in the call change the minimum repeats for mono-, di-, tri-, tetra-, penta-, hexa-nucleotide repeats
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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36 ssrs = pytrf.STRFinder(name, seq, 10, 6, 4, 3, 3, 3)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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37 NOTE: Dinucleotides GA and AG are reported separately by https://github.com/marbl/seqrequester.
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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38 The reversed pair STRs are about as common in the documentation sample.
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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39 Sequence read bias might be influenced by GC density or some other specific motif.
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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40 """
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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41 bed = []
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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42 wig = []
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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43 chrlens = {}
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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44 specific = None
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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45 if args.specific:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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46 specific = args.specific.upper().split(",")
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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47 fa = Fastx(args.fasta, uppercase=True)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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48 for name, seq in fa:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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49 chrlen = len(seq)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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50 chrlens[name] = chrlen
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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51 cbed = []
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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52 for ssr in pytrf.STRFinder(
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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53 name,
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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54 seq,
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55 args.monomin,
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56 args.dimin,
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57 args.trimin,
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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58 args.tetramin,
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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59 args.pentamin,
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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60 args.hexamin,
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61 ):
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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62 row = (
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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63 ssr.chrom,
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64 ssr.start,
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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65 ssr.end,
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66 ssr.motif,
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67 ssr.repeat,
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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68 ssr.length,
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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69 )
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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70 if args.specific and ssr.motif in specific:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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71 cbed.append(row)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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72 elif args.mono and len(ssr.motif) == 1:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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73 cbed.append(row)
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74 elif args.di and len(ssr.motif) == 2:
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75 cbed.append(row)
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76 elif args.tri and len(ssr.motif) == 3:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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77 cbed.append(row)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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78 elif args.tetra and len(ssr.motif) == 4:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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79 cbed.append(row)
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80 elif args.penta and len(ssr.motif) == 5:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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81 cbed.append(row)
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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82 elif args.hexa and len(ssr.motif) == 6:
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83 cbed.append(row)
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84 if args.bigwig:
dee16d45a2a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
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85 w = getDensity(name, cbed, chrlen, args.winwidth)
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86 wig.extend(w)
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87 bed.extend(cbed)
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88 if args.bigwig:
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89 wig.sort()
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90 with open("temp.bedg", "w") as bw:
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91 for row in wig:
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92 bw.write("%s %d %d %.2f\n" % row)
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93 chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
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94 with open("temp.chromlen", "w") as cl:
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95 cl.write("\n".join(chroms))
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96 cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", args.bed]
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97 subprocess.run(cmd)
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98 else:
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99 bed.sort()
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100 with open(args.bed, "w") as outbed:
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101 for row in bed:
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102 outbed.write("%s\t%d\t%d\t%s_%d\t%d\n" % row)
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103
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104
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105 if __name__ == "__main__":
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106 parser = argparse.ArgumentParser()
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107 a = parser.add_argument
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108 a("--di", action="store_true")
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109 a("--tri", action="store_true")
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110 a("--tetra", action="store_true")
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111 a("--penta", action="store_true")
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112 a("--hexa", action="store_true")
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113 a("--mono", action="store_true")
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114 a("--dimin", default=2, type=int)
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115 a("--trimin", default=2, type=int)
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116 a("--tetramin", default=2, type=int)
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117 a("--pentamin", default=2, type=int)
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118 a("--hexamin", default=2, type=int)
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119 a("--monomin", default=2, type=int)
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120 a("-f", "--fasta", default="humsamp.fa")
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121 a("-b", "--bed", default="humsamp.bed")
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122 a("--bigwig", action="store_true")
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123 a("--winwidth", default=128, type=int)
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124 a("--specific", default=None)
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125 a("--minreps", default=2, type=int)
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126 args = parser.parse_args()
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127 write_ssrs(args)